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Wednesday, July 29, 2009

Aligner tests

You know what I'd kill for? A simple set of tests for each aligner available. I have no idea why we didn't do this ages ago. I'm sick of off-by-one errors caused by all sorts of slightly different formats available - and I can't do unit tests without a good simple demonstration file for each aligner type.

I know Sam format should help with this - assuming everyone adopts it - but even for SAM I don't have a good control file.

I've asked someone here to set up this test using a known sequence- and if it works, I'll bundle the results into the Vancouver Package so everyone can use it.

Here's the 50-mer I picked to do the test. For those of you with some knowledge of cancer, it comes from tp53. It appears to blast uniquely to this location only.

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About Me

Anthony's new blog can be found at http://blogs.nature.com/fejes
While writing this blog, Anthony was a PhD Candidate at the University of British Columbia working at the BC Cancer Agency's Genome Sciences Centre. His area of interest is in second generation sequencing applications and bioinformatics algorithm development.